Can a Cohen marry a bat niddah? Are Cohens generally restricted from marrying baalei teshuva because of the possibility that they may be b'not niddah?
The Shulchan Aruch Even HaEzer 4:13 says that a ben or bat niddah is 'pagum' (defective). The Beit Shemuel, Chelkat Mechokek and Gra (the major commentaries there) all say that this is not to exclude them from a kohein.
I've never seen any restriction brought down in halacha that would prohibit a Cohen from marrying a Bat Niddah.
Moreover, the application of Ben/Bat Niddah has been severly downplayed by 20th century poskim.
(All of the above quotes come verbatim from here , although I have learned them originally elsewhere)
The last point about not being a "niddah mide'oraita" is significant: Technically, a woman must have r'iah (seeing) AND hargasha (an internal sensation) to qualify as an actual niddah. It could very well be that in our times, no woman is ever a Torah-level niddah.
So one on hand, we still treat the prohibition of sleeping with a niddah very seriously, because even the possibility of kares (spiritual excision) is a serious matter.
On the other hand, AFTER THE FACT, there are many reasons to say that no one is truly a ben/bat niddah nowadays.